Current genetic differentiation of Coffea canephoraPierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities

Céline Gomez,Valérie Poncet,Stéphane Dussert,Alexandre De Kochko,Perla Hamon,Serge Hamon

doi:10.1186/1471-2148-9-167

Abstract

BackgroundAmong Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone.ResultsBoth markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild C. canephora genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals.ConclusionOur data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between C. canephora diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities.

Highlights

Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests
Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation
Efficiency of restriction fragment length polymorphism (RFLP) and simple sequence repeats (SSRs) markers for polymorphism detection In the 107 sampled Coffea canephora accessions (Figure 1, table 1, and table 2), genetic polymorphism indexes (Na, HO and HE) at the 16 SSR loci and 8 RFLP loci were found to be highly variable throughout all geographic samples and types (Table 3)

Summary

Introduction

Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". The Guineo-Congolean regional center of endemism (Zone I on White's map, 1983) includes about 8,000 spp., about 80% of which are endemic. This zone corresponds to one of the 34 biodiversity hotspots defined by Mittermeier et al [5]: the Guinean (page number not for citation purposes). Through a study of the African Rubiaceae genera distribution, Robbrecht [13] gave additional support in favour of the refuge area concept, and demonstrated the importance of fluvial refugia in some taxa

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Conclusion